load Brgo.v3.0anno.Atgoslim.BP.list

load(file.path("..","Annotation_copy","output","v3.0annotation","Brgo.v3.0anno.Atgoslim.BP.list.Rdata"))

load GO.ORA function

GOseq function for Brassica rapa (v3.0)

# GOseq
library(ShortRead);library(goseq);library(GO.db);library("annotate")
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## Loading required package: Rsamtools
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## Loading required package: SummarizedExperiment
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: DelayedArray
## Loading required package: matrixStats
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##     select
## Loading required package: XML
# for ggplot heatmap
## uncompress gz file
system(paste("gunzip -c ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.gz")," > ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")))
## read cDNA fasta file 
Bra.v3.0_cdna<-readDNAStringSet(file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")) # copied from /Volumes/data_work/Data8/NGS_related/Brassica_rapa_Upendra/G3
Bra.v3.0_cdna
##   A DNAStringSet instance of length 46250
##         width seq                                           names               
##     [1]  1254 ATGCGACCACCGGGTGTTGTT...GAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
##     [2]  1668 ATGCCAGCAATGCATGCCGTT...AGATGGATCACAAAAGATTAA BraA01g000020.3C
##     [3]   957 ATGATGCTTCTCGTTCATACC...AACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
##     [4]  1299 ATGAGTCGTCTTCTCCTTGCT...GGGTCACGAGATGAGCTATAA BraA01g000040.3C
##     [5]   774 ATGGATTCTGGGCTTCAGCAT...GGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
##     ...   ... ...
## [46246]   162 ATGCGTCCGTCCTCAGCTCCC...TCTTTGGTGGTCCGGTTCTAA BraAnng001840.3C
## [46247]  1455 ATGTCTAATCAAGGATCAGGA...ACAGGTTTGTTTAGGTGCTAA BraAnng001850.3C
## [46248]  1011 ATGGACAACGTAATTCTGAAA...TCAGGGAAGAAAAGCCCCTGA BraAnng006150.3C
## [46249]   870 ATGTTTCCAAGACGTACAAGG...AGCAGTTGTCCTTATAGTTAG BraAnng000040.3C
## [46250]  1338 ATGCCGCAACAATACTGGAAC...GGAGAGAACCTTATCTCCTGA BraAnng003440.3C
## remove fasta file
system(paste("rm ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa"),sep=""))
# GOseq function
GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA<-function(genelist,padjust=0.05,ontology="BP",custom.category.list=Brgo.v3.0anno.Atgoslim.BP.list,Br_cdna=Bra.v3.0_cdna) { # return GO enrichment table, padjus, padjust=0.05. 
  
  bias<-nchar(Br_cdna)
  names(bias)<-names(Br_cdna)
  TF<-(names(bias) %in% genelist)*1
  names(TF)<-names(bias)
  #print(TF)
  pwf<-nullp(TF,bias.data=bias)
  #print(pwf$DEgenes)
  GO.pval <- goseq(pwf,gene2cat=custom.category.list,use_genes_without_cat=TRUE) # format became different in new goseq version (021111). Does not work (042716)
  #GO.pval <- goseq(pwf,gene2cat=Brgo.DF3,use_genes_without_cat=TRUE) # format became different in new goseq version (021111)
  
  #head(GO.pval) 
  if(ontology=="BP") {
    GO.pval2<-subset(GO.pval,ontology=="BP")
  } else if(ontology=="CC") {
    GO.pval2<-subset(GO.pval,ontology=="CC")
  } else {
    GO.pval2<-subset(GO.pval,ontology=="MF")
  }
    
  GO.pval2$over_represented_padjust<-p.adjust(GO.pval2$over_represented_pvalue,method="BH")
  if(GO.pval2$over_represented_padjust[1]>padjust) return("no enriched GO")
  else {
    enriched.GO<-GO.pval2[GO.pval2$over_represented_padjust<padjust,] 
    print("enriched.GO is")
    print(enriched.GO)
    
    ## write Term and Definition 
    for(i in 1:dim(enriched.GO)[1]) {
      if(is.null(Term(GOTERM[enriched.GO[i,"category"]]))) {next} else {
      enriched.GO$Term[i]<-Term(GOTERM[[enriched.GO[i,"category"]]])
      enriched.GO$Definition[i]<-Definition(GOTERM[[enriched.GO[i,"category"]]])
      }
    }
    return(enriched.GO)
  }
}
#
head(Bra.v3.0_cdna)
##   A DNAStringSet instance of length 6
##     width seq                                               names               
## [1]  1254 ATGCGACCACCGGGTGTTGTTTC...CTGAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2]  1668 ATGCCAGCAATGCATGCCGTTTT...GTAGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3]   957 ATGATGCTTCTCGTTCATACCCG...GGAACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4]  1299 ATGAGTCGTCTTCTCCTTGCTCA...GTGGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5]   774 ATGGATTCTGGGCTTCAGCATCT...AAGGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## [6]  3327 ATGGCGTCCACTCCTCCTCAAAA...GCGGTGGGTTTCAATTTCCTTGA BraA01g000060.3C
# length(bias) # 44239 > 45019 where the bias come from?
#  bias.data vector must have the same length as DEgenes vector!

ORA: two afternoon and expression pattern

twoafternoon.trtlive.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.trtlive.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
##   genes = col_character(),
##   logFC = col_double(),
##   logCPM = col_double(),
##   LR = col_double(),
##   PValue = col_double(),
##   FDR = col_double(),
##   AGI = col_character(),
##   At_symbol = col_character(),
##   At_short_description = col_character(),
##   perc_ID = col_double()
## )
  library(dplyr)
  #genelist.up<-base::get(paste("../output/",DEG.objs.v3.0annotation.unique[n],sep="")) %>% rownames_to_column() %>%  dplyr::filter(logFC>0) # does not work
    temp<-twoafternoon.trtlive.DEGs.all.v3.0anno
    genelist.up<-temp[temp[,"logFC"]>0&temp[,"FDR"]<0.05,"genes"];genelist.down<-temp[temp[,"logFC"]<0&temp[,"FDR"]<0.05,"genes"] 
    # check logFC value () 
    temp[temp[,3]>0&temp[,3]<0.05,"logFC"] # previous version (before Feb 7, 2020)
    temp[temp[,"logFC"]>0&temp[,"FDR"]<0.05,"logFC"] # revised version (after Feb 7, 2020)
   print(paste("number of up genes is ",dim(genelist.up)[1]))
## [1] "number of up genes is  459"
  # expression pattern of upregulated genes
   gene.of.interest.FDR.up <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC>0) %>%
     dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
   print("logFC>0")
## [1] "logFC>0"
   p.up1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[1,]);p.up1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[2,]);p.up2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[3,]);p.up3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[4,]);p.up4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[5,]);p.up5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

  # expression pattern of diwbregulated genes
   gene.of.interest.FDR.down <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC<0) %>% dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
   print("logFC<0")
## [1] "logFC<0"
   p.down1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[1,]);p.down1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[2,]);p.down2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[3,]);p.down3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[4,]);p.down4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[5,]);p.down5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

    #genelist.down<-read_csv(paste("../output/",file,sep=""))  %>%  dplyr::filter(logFC.genotypeR500<0)
   if(dim(genelist.up)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.up<-"no enriched GO";next} else {GO.ORA.temp.up<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.up)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns

## [1] "enriched.GO is"
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 3164 GO:0071732            6.820561e-08                1.0000000          8
## 3114 GO:0071369            2.089131e-07                1.0000000          8
## 1195 GO:0010167            1.021437e-06                0.9999999          7
## 3094 GO:0071281            1.955280e-06                0.9999998          8
## 1530 GO:0016036            7.136493e-06                0.9999990         10
## 254  GO:0006096            2.202118e-05                0.9999970          9
## 1445 GO:0015706            8.135340e-05                0.9999948          5
##      numInCat                                      term ontology
## 3164       52         cellular response to nitric oxide       BP
## 3114       62    cellular response to ethylene stimulus       BP
## 1195       53                       response to nitrate       BP
## 3094       77             cellular response to iron ion       BP
## 1530      148 cellular response to phosphate starvation       BP
## 254       138                        glycolytic process       BP
## 1445       39                         nitrate transport       BP
##      over_represented_padjust
## 3164             0.0002584311
## 3114             0.0003957859
## 1195             0.0012900754
## 3094             0.0018521386
## 1530             0.0054080343
## 254              0.0139063745
## 1445             0.0440354306
      print(paste("number of down genes is ",dim(genelist.down)[1]))
## [1] "number of down genes is  1015"
   if(dim(genelist.down)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.down<-"no enriched GO"; next} else {GO.ORA.temp.down<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.down)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns

## [1] "enriched.GO is"
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200            4.504540e-16                1.0000000         35
## 2253 GO:0042742            5.385608e-14                1.0000000         56
## 638  GO:0006952            7.545274e-13                1.0000000         72
## 2750 GO:0050832            2.359748e-11                1.0000000         37
## 890  GO:0009611            5.566564e-11                1.0000000         36
## 3708 GO:2000022            2.000124e-10                1.0000000         16
## 899  GO:0009626            6.561878e-10                1.0000000         20
## 423  GO:0006468            2.148206e-09                1.0000000         81
## 853  GO:0009407            2.454257e-08                1.0000000         11
## 1166 GO:0010112            2.807664e-08                1.0000000          8
## 557  GO:0006749            1.255567e-07                1.0000000         12
## 894  GO:0009617            1.473423e-07                1.0000000         22
## 1174 GO:0010120            2.496944e-07                1.0000000          8
## 972  GO:0009751            4.766890e-07                0.9999999         25
## 900  GO:0009627            6.998144e-07                0.9999999         13
## 855  GO:0009409            1.752277e-06                0.9999993         37
## 1038 GO:0009871            3.976235e-06                0.9999999          5
## 1858 GO:0031348            5.987811e-06                0.9999992         10
## 1857 GO:0031347            8.866320e-06                0.9999986         11
## 646  GO:0006979            1.247452e-05                0.9999955         28
## 3442 GO:1900067            1.481476e-05                1.0000000          3
## 1183 GO:0010150            2.707898e-05                0.9999927         17
## 1107 GO:0010030            2.844214e-05                0.9999967          8
## 49   GO:0000272            3.213706e-05                0.9999970          7
## 2986 GO:0062034            3.975137e-05                0.9999991          4
## 2439 GO:0045332            4.455056e-05                0.9999967          6
## 185  GO:0002229            5.052194e-05                0.9999887         13
## 2859 GO:0051707            9.404250e-05                0.9999827         10
## 234  GO:0006032            9.606073e-05                0.9999914          6
## 1460 GO:0015749            1.074678e-04                0.9999934          5
## 478  GO:0006562            1.084541e-04                0.9999992          3
## 1291 GO:0010345            1.123459e-04                0.9999869          7
## 619  GO:0006887            1.685980e-04                0.9999666         10
## 921  GO:0009651            1.797603e-04                0.9999078         44
## 3251 GO:0080142            1.838731e-04                0.9999872          5
## 944  GO:0009697            1.865949e-04                0.9999867          5
## 859  GO:0009414            2.028253e-04                0.9999119         29
## 1001 GO:0009816            2.098586e-04                0.9999573         10
## 2617 GO:0048194            2.349755e-04                0.9999825          5
## 1177 GO:0010133            2.697046e-04                0.9999958          3
## 1030 GO:0009862            2.758968e-04                0.9999781          5
## 2247 GO:0042593            3.361831e-04                0.9999921          3
## 1002 GO:0009817            3.842136e-04                0.9999234          9
## 187  GO:0002237            4.003418e-04                0.9999202          9
## 2223 GO:0042344            4.121584e-04                0.9999773          4
## 1859 GO:0031349            4.498132e-04                0.9999756          4
## 2794 GO:0051258            5.343753e-04                0.9999875          3
## 2917 GO:0055114            5.773902e-04                0.9996410         71
##      numInCat
## 1210      286
## 2253      726
## 638      1165
## 2750      469
## 890       419
## 3708       89
## 899       140
## 423      1484
## 853        67
## 1166       22
## 557        85
## 894       241
## 1174       27
## 972       347
## 900       104
## 855       696
## 1038       11
## 1858       64
## 1857       95
## 646       502
## 3442        3
## 1183      219
## 1107       54
## 49         39
## 2986        8
## 2439       23
## 185       126
## 2859       97
## 234        35
## 1460       18
## 478         4
## 1291       41
## 619        96
## 921      1045
## 3251       19
## 944        21
## 859       596
## 1001       97
## 2617       20
## 1177        5
## 1030       24
## 2247        8
## 1002      100
## 187        88
## 2223       15
## 1859       13
## 2794        6
## 2917     1923
##                                                                                               term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 638                                                                               defense response
## 2750                                                                    defense response to fungus
## 890                                                                           response to wounding
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 899                                                             plant-type hypersensitive response
## 423                                                                        protein phosphorylation
## 853                                                                        toxin catabolic process
## 1166                                                    regulation of systemic acquired resistance
## 557                                                                  glutathione metabolic process
## 894                                                                          response to bacterium
## 1174                                                                camalexin biosynthetic process
## 972                                                                     response to salicylic acid
## 900                                                                   systemic acquired resistance
## 855                                                                               response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858                                                       negative regulation of defense response
## 1857                                                                regulation of defense response
## 646                                                                   response to oxidative stress
## 3442                                                regulation of cellular response to alkaline pH
## 1183                                                                               leaf senescence
## 1107                                                       positive regulation of seed germination
## 49                                                                polysaccharide catabolic process
## 2986                                                         L-pipecolic acid biosynthetic process
## 2439                                                                    phospholipid translocation
## 185                                                                  defense response to oomycetes
## 2859                                                                    response to other organism
## 234                                                                       chitin catabolic process
## 1460                                                        monosaccharide transmembrane transport
## 478                                                                      proline catabolic process
## 1291                                                                  suberin biosynthetic process
## 619                                                                                     exocytosis
## 921                                                                        response to salt stress
## 3251                                             regulation of salicylic acid biosynthetic process
## 944                                                            salicylic acid biosynthetic process
## 859                                                                  response to water deprivation
## 1001                                       defense response to bacterium, incompatible interaction
## 2617                                                                         Golgi vesicle budding
## 1177                                                        proline catabolic process to glutamate
## 1030                       systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247                                                                           glucose homeostasis
## 1002                                          defense response to fungus, incompatible interaction
## 187                                                       response to molecule of bacterial origin
## 2223                                                        indole glucosinolate catabolic process
## 1859                                                       positive regulation of defense response
## 2794                                                                        protein polymerization
## 2917                                                                   oxidation-reduction process
##      ontology over_represented_padjust
## 1210       BP             1.706770e-12
## 2253       BP             1.020303e-10
## 638        BP             9.529681e-10
## 2750       BP             2.235271e-08
## 890        BP             4.218342e-08
## 3708       BP             1.263079e-07
## 899        BP             3.551851e-07
## 423        BP             1.017444e-06
## 853        BP             1.033242e-05
## 1166       BP             1.063824e-05
## 557        BP             4.324859e-05
## 894        BP             4.652334e-05
## 1174       BP             7.277632e-05
## 972        BP             1.290125e-04
## 900        BP             1.767731e-04
## 855        BP             4.149611e-04
## 1038       BP             8.862326e-04
## 1858       BP             1.260434e-03
## 1857       BP             1.768131e-03
## 646        BP             2.363297e-03
## 3442       BP             2.673007e-03
## 1183       BP             4.663739e-03
## 1107       BP             4.685533e-03
## 49         BP             5.073638e-03
## 2986       BP             6.024717e-03
## 2439       BP             6.492387e-03
## 185        BP             7.089912e-03
## 2859       BP             1.255083e-02
## 234        BP             1.255083e-02
## 1460       BP             1.325589e-02
## 478        BP             1.325589e-02
## 1291       BP             1.330246e-02
## 619        BP             1.935812e-02
## 921        BP             1.963911e-02
## 3251       BP             1.963911e-02
## 944        BP             1.963911e-02
## 859        BP             2.077041e-02
## 1001       BP             2.092512e-02
## 2617       BP             2.282878e-02
## 1177       BP             2.549690e-02
## 1030       BP             2.549690e-02
## 2247       BP             3.032851e-02
## 1002       BP             3.385547e-02
## 187        BP             3.447489e-02
## 2223       BP             3.470374e-02
## 1859       BP             3.705092e-02
## 2794       BP             4.307975e-02
## 2917       BP             4.557774e-02
    # handling "no enriched GO" 
    # genelist.names<-c("GO.ORA.temp.up_down","GO.ORA.temp.down_up") # test
    x<-list(GO.ORA.temp.up=GO.ORA.temp.up,
            GO.ORA.temp.down=GO.ORA.temp.down) # list
    # x<-x[!x=="no enriched GO"] # remove "no enriched GO" result
    ## add sample info and FC info and save GO.ORA result
        if(length(x)==0) {next} else {GO.ORA.result<-x}
GO.ORA.result      
## $GO.ORA.temp.up
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 3164 GO:0071732            6.820561e-08                1.0000000          8
## 3114 GO:0071369            2.089131e-07                1.0000000          8
## 1195 GO:0010167            1.021437e-06                0.9999999          7
## 3094 GO:0071281            1.955280e-06                0.9999998          8
## 1530 GO:0016036            7.136493e-06                0.9999990         10
## 254  GO:0006096            2.202118e-05                0.9999970          9
## 1445 GO:0015706            8.135340e-05                0.9999948          5
##      numInCat                                      term ontology
## 3164       52         cellular response to nitric oxide       BP
## 3114       62    cellular response to ethylene stimulus       BP
## 1195       53                       response to nitrate       BP
## 3094       77             cellular response to iron ion       BP
## 1530      148 cellular response to phosphate starvation       BP
## 254       138                        glycolytic process       BP
## 1445       39                         nitrate transport       BP
##      over_represented_padjust                                      Term
## 3164             0.0002584311         cellular response to nitric oxide
## 3114             0.0003957859    cellular response to ethylene stimulus
## 1195             0.0012900754                       response to nitrate
## 3094             0.0018521386             cellular response to iron ion
## 1530             0.0054080343 cellular response to phosphate starvation
## 254              0.0139063745                        glycolytic process
## 1445             0.0440354306                         nitrate transport
##                                                                                                                                                                                                                                                                                                                                                                                                                                          Definition
## 3164                                                                                                                                                                                                                                                        Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
## 3114                                                                                                                                                                                                                                                  Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethylene (ethene) stimulus.
## 1195                                                                                                                                                                                                                                              Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrate stimulus.
## 3094                                                                                                                                                                                                                                                           Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
## 1530                                                                                                                                                                                                                                                       Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
## 254  The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
## 1445                                                                                                                                                                                                                                                                                                        The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
## 
## $GO.ORA.temp.down
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200            4.504540e-16                1.0000000         35
## 2253 GO:0042742            5.385608e-14                1.0000000         56
## 638  GO:0006952            7.545274e-13                1.0000000         72
## 2750 GO:0050832            2.359748e-11                1.0000000         37
## 890  GO:0009611            5.566564e-11                1.0000000         36
## 3708 GO:2000022            2.000124e-10                1.0000000         16
## 899  GO:0009626            6.561878e-10                1.0000000         20
## 423  GO:0006468            2.148206e-09                1.0000000         81
## 853  GO:0009407            2.454257e-08                1.0000000         11
## 1166 GO:0010112            2.807664e-08                1.0000000          8
## 557  GO:0006749            1.255567e-07                1.0000000         12
## 894  GO:0009617            1.473423e-07                1.0000000         22
## 1174 GO:0010120            2.496944e-07                1.0000000          8
## 972  GO:0009751            4.766890e-07                0.9999999         25
## 900  GO:0009627            6.998144e-07                0.9999999         13
## 855  GO:0009409            1.752277e-06                0.9999993         37
## 1038 GO:0009871            3.976235e-06                0.9999999          5
## 1858 GO:0031348            5.987811e-06                0.9999992         10
## 1857 GO:0031347            8.866320e-06                0.9999986         11
## 646  GO:0006979            1.247452e-05                0.9999955         28
## 3442 GO:1900067            1.481476e-05                1.0000000          3
## 1183 GO:0010150            2.707898e-05                0.9999927         17
## 1107 GO:0010030            2.844214e-05                0.9999967          8
## 49   GO:0000272            3.213706e-05                0.9999970          7
## 2986 GO:0062034            3.975137e-05                0.9999991          4
## 2439 GO:0045332            4.455056e-05                0.9999967          6
## 185  GO:0002229            5.052194e-05                0.9999887         13
## 2859 GO:0051707            9.404250e-05                0.9999827         10
## 234  GO:0006032            9.606073e-05                0.9999914          6
## 1460 GO:0015749            1.074678e-04                0.9999934          5
## 478  GO:0006562            1.084541e-04                0.9999992          3
## 1291 GO:0010345            1.123459e-04                0.9999869          7
## 619  GO:0006887            1.685980e-04                0.9999666         10
## 921  GO:0009651            1.797603e-04                0.9999078         44
## 3251 GO:0080142            1.838731e-04                0.9999872          5
## 944  GO:0009697            1.865949e-04                0.9999867          5
## 859  GO:0009414            2.028253e-04                0.9999119         29
## 1001 GO:0009816            2.098586e-04                0.9999573         10
## 2617 GO:0048194            2.349755e-04                0.9999825          5
## 1177 GO:0010133            2.697046e-04                0.9999958          3
## 1030 GO:0009862            2.758968e-04                0.9999781          5
## 2247 GO:0042593            3.361831e-04                0.9999921          3
## 1002 GO:0009817            3.842136e-04                0.9999234          9
## 187  GO:0002237            4.003418e-04                0.9999202          9
## 2223 GO:0042344            4.121584e-04                0.9999773          4
## 1859 GO:0031349            4.498132e-04                0.9999756          4
## 2794 GO:0051258            5.343753e-04                0.9999875          3
## 2917 GO:0055114            5.773902e-04                0.9996410         71
##      numInCat
## 1210      286
## 2253      726
## 638      1165
## 2750      469
## 890       419
## 3708       89
## 899       140
## 423      1484
## 853        67
## 1166       22
## 557        85
## 894       241
## 1174       27
## 972       347
## 900       104
## 855       696
## 1038       11
## 1858       64
## 1857       95
## 646       502
## 3442        3
## 1183      219
## 1107       54
## 49         39
## 2986        8
## 2439       23
## 185       126
## 2859       97
## 234        35
## 1460       18
## 478         4
## 1291       41
## 619        96
## 921      1045
## 3251       19
## 944        21
## 859       596
## 1001       97
## 2617       20
## 1177        5
## 1030       24
## 2247        8
## 1002      100
## 187        88
## 2223       15
## 1859       13
## 2794        6
## 2917     1923
##                                                                                               term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 638                                                                               defense response
## 2750                                                                    defense response to fungus
## 890                                                                           response to wounding
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 899                                                             plant-type hypersensitive response
## 423                                                                        protein phosphorylation
## 853                                                                        toxin catabolic process
## 1166                                                    regulation of systemic acquired resistance
## 557                                                                  glutathione metabolic process
## 894                                                                          response to bacterium
## 1174                                                                camalexin biosynthetic process
## 972                                                                     response to salicylic acid
## 900                                                                   systemic acquired resistance
## 855                                                                               response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858                                                       negative regulation of defense response
## 1857                                                                regulation of defense response
## 646                                                                   response to oxidative stress
## 3442                                                regulation of cellular response to alkaline pH
## 1183                                                                               leaf senescence
## 1107                                                       positive regulation of seed germination
## 49                                                                polysaccharide catabolic process
## 2986                                                         L-pipecolic acid biosynthetic process
## 2439                                                                    phospholipid translocation
## 185                                                                  defense response to oomycetes
## 2859                                                                    response to other organism
## 234                                                                       chitin catabolic process
## 1460                                                        monosaccharide transmembrane transport
## 478                                                                      proline catabolic process
## 1291                                                                  suberin biosynthetic process
## 619                                                                                     exocytosis
## 921                                                                        response to salt stress
## 3251                                             regulation of salicylic acid biosynthetic process
## 944                                                            salicylic acid biosynthetic process
## 859                                                                  response to water deprivation
## 1001                                       defense response to bacterium, incompatible interaction
## 2617                                                                         Golgi vesicle budding
## 1177                                                        proline catabolic process to glutamate
## 1030                       systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247                                                                           glucose homeostasis
## 1002                                          defense response to fungus, incompatible interaction
## 187                                                       response to molecule of bacterial origin
## 2223                                                        indole glucosinolate catabolic process
## 1859                                                       positive regulation of defense response
## 2794                                                                        protein polymerization
## 2917                                                                   oxidation-reduction process
##      ontology over_represented_padjust
## 1210       BP             1.706770e-12
## 2253       BP             1.020303e-10
## 638        BP             9.529681e-10
## 2750       BP             2.235271e-08
## 890        BP             4.218342e-08
## 3708       BP             1.263079e-07
## 899        BP             3.551851e-07
## 423        BP             1.017444e-06
## 853        BP             1.033242e-05
## 1166       BP             1.063824e-05
## 557        BP             4.324859e-05
## 894        BP             4.652334e-05
## 1174       BP             7.277632e-05
## 972        BP             1.290125e-04
## 900        BP             1.767731e-04
## 855        BP             4.149611e-04
## 1038       BP             8.862326e-04
## 1858       BP             1.260434e-03
## 1857       BP             1.768131e-03
## 646        BP             2.363297e-03
## 3442       BP             2.673007e-03
## 1183       BP             4.663739e-03
## 1107       BP             4.685533e-03
## 49         BP             5.073638e-03
## 2986       BP             6.024717e-03
## 2439       BP             6.492387e-03
## 185        BP             7.089912e-03
## 2859       BP             1.255083e-02
## 234        BP             1.255083e-02
## 1460       BP             1.325589e-02
## 478        BP             1.325589e-02
## 1291       BP             1.330246e-02
## 619        BP             1.935812e-02
## 921        BP             1.963911e-02
## 3251       BP             1.963911e-02
## 944        BP             1.963911e-02
## 859        BP             2.077041e-02
## 1001       BP             2.092512e-02
## 2617       BP             2.282878e-02
## 1177       BP             2.549690e-02
## 1030       BP             2.549690e-02
## 2247       BP             3.032851e-02
## 1002       BP             3.385547e-02
## 187        BP             3.447489e-02
## 2223       BP             3.470374e-02
## 1859       BP             3.705092e-02
## 2794       BP             4.307975e-02
## 2917       BP             4.557774e-02
##                                                                                               Term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 638                                                                               defense response
## 2750                                                                    defense response to fungus
## 890                                                                           response to wounding
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 899                                                             plant-type hypersensitive response
## 423                                                                        protein phosphorylation
## 853                                                                        toxin catabolic process
## 1166                                                    regulation of systemic acquired resistance
## 557                                                                  glutathione metabolic process
## 894                                                                          response to bacterium
## 1174                                                                camalexin biosynthetic process
## 972                                                                     response to salicylic acid
## 900                                                                   systemic acquired resistance
## 855                                                                               response to cold
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 1858                                                       negative regulation of defense response
## 1857                                                                regulation of defense response
## 646                                                                   response to oxidative stress
## 3442                                                regulation of cellular response to alkaline pH
## 1183                                                                               leaf senescence
## 1107                                                       positive regulation of seed germination
## 49                                                                polysaccharide catabolic process
## 2986                                                         L-pipecolic acid biosynthetic process
## 2439                                                                    phospholipid translocation
## 185                                                                  defense response to oomycetes
## 2859                                                                    response to other organism
## 234                                                                       chitin catabolic process
## 1460                                                        monosaccharide transmembrane transport
## 478                                                                      proline catabolic process
## 1291                                                                  suberin biosynthetic process
## 619                                                                                     exocytosis
## 921                                                                        response to salt stress
## 3251                                             regulation of salicylic acid biosynthetic process
## 944                                                            salicylic acid biosynthetic process
## 859                                                                  response to water deprivation
## 1001                                       defense response to bacterium, incompatible interaction
## 2617                                                                         Golgi vesicle budding
## 1177                                                        proline catabolic process to glutamate
## 1030                       systemic acquired resistance, salicylic acid mediated signaling pathway
## 2247                                                                           glucose homeostasis
## 1002                                          defense response to fungus, incompatible interaction
## 187                                                       response to molecule of bacterial origin
## 2223                                                        indole glucosinolate catabolic process
## 1859                                                       positive regulation of defense response
## 2794                                                                        protein polymerization
## 2917                                                                   oxidation-reduction process
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Definition
## 1210                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.
## 2253                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
## 638                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
## 2750                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
## 890                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
## 3708                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Any process that modulates the frequency, rate or extent of jasmonic acid mediated signaling pathway.
## 899                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        The rapid, localized death of plant cells in response to invasion by a pathogen.
## 423                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           The process of introducing a phosphate group on to a protein.
## 853                                                                                                                                                                                                                                                                                                                                                                                                                                                          The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
## 1166                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Any process that modulates the frequency, rate or extent of systemic acquired resistance.
## 557                                                                                                                                                                                                                                                                                                                  The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
## 894                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
## 1174                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
## 972                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
## 900                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             The salicylic acid mediated response to a pathogen which confers broad spectrum resistance.
## 855                                                                                                                                                                                                                                                                                                                                                                                                                                  Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
## 1038                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        The series of molecular signals mediated by ethylene (ethene) involved in jasmonic acid/ethylene dependent systemic resistance.
## 1858                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response.
## 1857                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        Any process that modulates the frequency, rate or extent of a defense response.
## 646                                                                                                                                                                                                                                                                                                                                               Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
## 3442                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   <NA>
## 1183                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.
## 1107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Any process that activates or increase the rate of seed germination.
## 49                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
## 2986                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            The chemical reactions and pathways resulting in the formation of L-pipecolic acid, a metabolite of lysine.
## 2439                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.
## 185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Reactions triggered in response to the presence of oomycetes that act to protect the cell or organism.
## 2859                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
## 234                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
## 1460                                                                                                                                                                                                                                                                                                                           The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
## 478                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
## 1291                                                                                                                                                                                                                                                                                                                                                                                                                                                                  The chemical reactions and pathways resulting in the formation of suberin monomers and suberin polyesters. Suberin monomers are derived from fatty acids and trans-cinnamic acids. The monomers are then cross-linked with glycerols.
## 619  A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
## 921                                                                                                                                                                                                                                                                                                                                                                Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
## 3251                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of salicylic acid.
## 944                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 The chemical reactions and pathways resulting in the formation of salicylic acid (2-hydroxybenzoic acid), a derivative of benzoic acid.
## 859                                                                                                                                                                                                                                                                                                                                                                                                                                                             Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water.
## 1001                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            A response of an organism to a bacterium that prevents the occurrence or spread of disease.
## 2617                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            The evagination of the Golgi membrane, resulting in formation of a vesicle.
## 1177                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.
## 1030                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   The series of molecular signals mediated by salicylic acid involved in systemic acquired resistance.
## 2247                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
## 1002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               A response of an organism to a fungus that prevents the occurrence or spread of disease.
## 187                                                                                                                                                                                                                                                                                                                                                                                                                                      Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
## 2223                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        The chemical reactions and pathways resulting in the breakdown of indole glucosinolates, sulfur-containing compounds that have a common structure linked to an R group derived from tryptophan.
## 1859                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Any process that activates or increases the frequency, rate or extent of a defense response.
## 2794                                                                                                                                                                                                                                                                                                                                                                                                                        The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
## 2917                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
# save data           
save(GO.ORA.result,file="../output/GOseq.timecourse.twoafternoon.Brgo.v3.0.Atgoslim.BP.list.enrich.Rdata")

session info

sessionInfo
## function (package = NULL) 
## {
##     z <- list()
##     z$R.version <- R.Version()
##     z$platform <- z$R.version$platform
##     if (nzchar(.Platform$r_arch)) 
##         z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
##     z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, 
##         "-bit)")
##     z$locale <- Sys.getlocale()
##     z$running <- osVersion
##     z$RNGkind <- RNGkind()
##     if (is.null(package)) {
##         package <- grep("^package:", search(), value = TRUE)
##         keep <- vapply(package, function(x) x == "package:base" || 
##             !is.null(attr(as.environment(x), "path")), NA)
##         package <- .rmpkg(package[keep])
##     }
##     pkgDesc <- lapply(package, packageDescription, encoding = NA)
##     if (length(package) == 0) 
##         stop("no valid packages were specified")
##     basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
##         x$Priority == "base")
##     z$basePkgs <- package[basePkgs]
##     if (any(!basePkgs)) {
##         z$otherPkgs <- pkgDesc[!basePkgs]
##         names(z$otherPkgs) <- package[!basePkgs]
##     }
##     loadedOnly <- loadedNamespaces()
##     loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
##     if (length(loadedOnly)) {
##         names(loadedOnly) <- loadedOnly
##         pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
##         z$loadedOnly <- pkgDesc[loadedOnly]
##     }
##     z$matprod <- as.character(options("matprod"))
##     es <- extSoftVersion()
##     z$BLAS <- as.character(es["BLAS"])
##     z$LAPACK <- La_library()
##     class(z) <- "sessionInfo"
##     z
## }
## <bytecode: 0x7fe3cbcc1b98>
## <environment: namespace:utils>